Freesurfer May 2008

freesurfer@nmr.mgh.harvard.edu

63 participants
95 discussions

tksurfer display broken
by Juranek, Jenifer 27 May '08

27 May '08

Hi, I recently encountered a problem with tksurfer display (worked perfectly fine a couple of weeks ago). The only change I've made to my linux (centOs 5) system is the recent installation of MATLAB r2008a. Just a note: This was *not* a fun process since the MATLAB 2008a install required deprecated libs (e.g. libXp) which are no longer included with RHEL5. Bottom line: the beginning of my tksurfer display problem does coincide with this process of attempting to install MATLAB r2008a. Although I finally succeeded in getting the MATLAB installed, is there a fix to restore tksurfer display to its proper functionality? In descriptive terms, the tksurfer command launches a window containing a small sliver of the posterior region of the brain. Screen output is pasted below for calling up "bert". This morning I upgraded from freesurfer v403 to v404, but the problem still persists. I suspect I broke something in my RHEL5 while trying to fix the Matlab r2008a install failure. BTW..."bert" looks fine in tkmedit (including aseg+aparc file) Any ideas? Jenifer [jjuranek@localhost freesurfer]$ tksurfer bert rh pial surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /usr/local/freesurfer surfer: Reading header info from /usr/local/freesurfer/subjects/bert/mri/T1.mgz surfer: vertices=131848, faces=263692 Loading /usr/local/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(bert) surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations...

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freesurfer version 3.0 ?
by Lars M. Rimol 27 May '08

27 May '08

Hi, We have a dataset that was processed (by somebody else) with an old freesurfer version and we need to find out exactly which version was used. We have a freesurfer_3.0 directory (and a freesurfer-Linux-centos4-stable-v3.0-full.tar.gz download) with a build-stamp.txt that says: freesurfer-Linux-centos4-stable-v3.0 Is the final digit just missing, or was this a version prior to 3.0.1? Thank you! -- yours, LMR

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cortical thickness
by Feng-Xian Yan 27 May '08

27 May '08

Hi, I have some questions about cortical thickness. What method does freesurfer calculate the cortical thickness? Can freesurfer provide the cortical thickness value at each voxel in the gray matter? Thank you in advance. Feng-Xian

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Color scheme settings frustratration
by Martin Kavec 27 May '08

27 May '08

Hi folks, I am scratching my head, how did you guys set the color scheme of the lgi overlay on: http://surfer.nmr.mgh.harvard.edu/fswiki/LGI the image with text "Example of lGI overlay on the brain using a colocoded scale" What I do is I load pial surface and overlay ?h.pial_lgi, but can not replicate the scheme on the webpage. Thanks, Martin

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S_subcentral_ant and aparcstats2table
by Juergen Haenggi 26 May '08

26 May '08

Dear FS experts With respect to the S_subcentral_ant label that is missed in some subjects but not in others (already discussed on the FS list), there is some unexpected behaviour of the aparcstats2table command that confused me. After using the aparcstats2table command on 33 subjects and importing the file.stats into SPSS there is some shift in the values due to the missing label S_subcentral_ant. This is not confusing. But when looking at the value (52 cm3) of S_precentralSuperiorpart of the last subject (see last line in attachment), I guess that this is the value of S_subcentral_post label. The actual value is shifted to the left that means there is another label missing left to S_precentralSuperiorpart. This is further complicated because in the 14th subject from above both S_subcentral_ant and post are missing. From the magnitude of the values it is not easy to guess which value belong to which label. Does anybody made similar experiences on this issue? What is the solution? Is there already an aparcstats2table command that accounts for that? It is very labour intensive and error-prone to control all the individual stats files and shift values!!! Sorry for inconvenience Thanks in advance Best regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

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4.0.4 install issue on RH9
by Mischka Gerken 23 May '08

23 May '08

Hi folks I'm having a hard time figuring out what this libexpat files is and what to do about it. I'm installing FS4.0.4 on a Linux RH9 machine. We've been running 4.0.1 just fine, but are hoping this build will fix some qdec issues. After install, this error message comes up regardless of what component we are trying to run (tksurfer, qdec, tkmedit, etc). Any thoughts? [xwang@mco321142 APL06L_longitudinal_analysis_200805]$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Linux-rh9-stable-pub-v4.0.4 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/xwang/freesurfer_4.0.4 FSFAST_HOME /home/xwang/freesurfer_4.0.4/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /home/xwang/freesurfer_4.0.4/subjects/APL06L_longitudinal_analysis_200805 MNI_DIR /home/xwang/freesurfer_4.0.4/mni/ FSL_DIR /home/xwang/bin/fsl-3.3.11 [xwang@mco321142 APL06L_longitudinal_analysis_200805]$ tkmedit APL06L650_20070603_AP0005583_S3_tp1b brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white *tkmedit.bin: error while loading shared libraries: libexpat.so.1: cannot open shared object file: No such file or directory *Many thanks! -Mischka.

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Entire brain tissue categorized as wm in grainy images
by Laluz, Victor 23 May '08

23 May '08

Hello, Occasionally I run into a problem with lower quality, noisy T1 images (1.5mmx1mmx1mm) where almost all of the tissue is classified as white matter. Upon inspecting these images (attached), I can understand why it would make this mistake; the white-gray matter border in them is very difficult to identify, and tissue intensity is almost homogenous, except for areas of partial voluming at the very outer edge (which is the only tissue contained by the pial surface - the white surface on these images). Is there any way I can force the white matter segmentation step to be more conservative with some of its settings? For example, could I modify the intensity "threshold" for the wm segmentation step? Since this isn't an error described in the wiki, I'm guessing control points won't do me much good. Any suggestions would be great. Victor Laluz : Imaging Coordinator : UCSF Memory and Aging Center

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Install two verson of freesurfer on one computer
by yczhang＠nlpr.ia.ac.cn 23 May '08

23 May '08

Dear Mr or Ms, I want to know whether I can install two versions of freesurfer on one computer. If I want to use one version,I just change the freesurfer home by "gedit .bashrc". If I want to use another,I change back to the former freesurfer home of another version. Whether they are compatible with each other? Thanks!

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Creating a volume with MRIS_FILL
by Cochrane Jamison 22 May '08

22 May '08

I am using mris_fill to create a volume from the lh.pial surface as well as the rh.pial surface. I have 2 questions: 1. How can I combine the 2 separate hemisphere volumes into a single full brain volume that I can export and view in analyze? I only know to use mri_convert on each one separately. Does this need to be done before I run mris_fill, or is there another combined surface that has the same resolution as the pial surfaces that I can run mris_fill on? 2. I know that when I run mris_fill, the volumes that are produced do not contain orientation information. When I load them into Analyze, the volume is mirrored and upside down. I was wondering how I can "get" orientation information back into the volume, and also correct the mirrored and upside down viewing issue. These results were produced by Freesurfer from standard dicom files from a volumetric scan. Thanks, Cochrane Jamison

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Combining two regions
by Pierson, Ronald K 22 May '08

22 May '08

I apologize if this has been asked and answered before, but I wish to combine rostral and caudal middle frontal gyri for a summary measure. To find the average thickness of the entire region, will it be weighted by the surface area or by the number of vertices? Avg_MidFront = ((CaudThick*NumVertsCaud) + (RostThick*NumVertsRost) / (NumVertsCaud + NumVertsRost)) Or Avg_MidFront = ((CaudThick*SurfAreaCaud) + (RostThick*SurfAreaRost) / (SurfAreaCaud + SurfAreaRost)) Thanks, Ronald Pierson Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you.

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Freesurfer May 2008